生物技术通报 ›› 2026, Vol. 42 ›› Issue (11): 134-144.doi: 10.13560/j.cnki.biotech.bull.1985.2025-1404

• 研究报告 • 上一篇    

蓝莓全基因组SSR引物开发及遗传多样性分析

刘思文1, 王博伟1, 邢金杰1, 王静2, 李亚东1, 孙海悦1()   

  1. 1.吉林农业大学园艺学院,长春 130118
    2.济南市公园发展服务中心百花公园,济南 250100
  • 收稿日期:2025-12-23 出版日期:2026-11-26 发布日期:2026-11-03
  • 通讯作者: 孙海悦haiyuesun@jlau.edu.cn
  • 基金资助:
    吉林省科技发展计划(20250202007NC);国家自然科学基金项目(32472695)

Genome-wide Development of SSR Primers and Genetic Diversity Analysis in Blueberry

LIU Si-wen1, WANG Bo-wei1, XING Jin-jie1, WANG Jing2, LI Ya-dong1, SUN Hai-yue1()   

  1. 1.College of Horticulture, Jilin Agricultural University, Changchun 130118
    2.Baihua Park of Jinan Park Development and Service Center, Jinan 250100
  • Received:2025-12-23 Published:2026-11-26 Online:2026-11-03

摘要:

目的 基于蓝莓品种形态易混淆、缺乏精准鉴定体系的问题,通过全基因组SSR位点的发掘及相关特性分析,开发新的SSR标记引物,为蓝莓种质精准鉴定和遗传多样性评价提供支撑。 方法 利用Krait软件对‘Draper’基因组SSR位点进行检索分析,并使用Primer 3.0软件设计引物,结合生物信息学技术初步筛选SSR标记引物。逐步扩大蓝莓种质数量进行PCR扩增,采用非变性聚丙烯酰胺凝胶电泳和毛细管电泳相结合的方式,筛选高多态性SSR标记引物,并进行蓝莓种质资源的遗传多样性分析。 结果 ‘Draper’基因组SSR位点发掘结果显示,共检测到888 906个SSR位点,以二核苷酸重复类型为主,占总SSR位点数的87.8%,三核苷酸次之,占总SSR位点数的6.34%。经生物信息学初步筛选,获得103对SSR标记引物;经多轮电泳筛选,最终获得17对高多态性SSR标记引物。利用这17对引物对64份蓝莓种质资源进行遗传多样性分析,共检测到204个等位基因,有效等位基因数(Ne)、Shannon’s信息指数(I)平均值分别为6.165和1.956;多态信息量(PIC)平均值为0.985,表明SSR标记多态性较高。UPGMA聚类分析显示,在Nei’s遗传距离0.000 8处,64份蓝莓种质资源可划分为3个聚类群。 结论 揭示了蓝莓基因组中SSR位点的数量和类型特性。获得17对高多态性SSR引物,可用于区分蓝莓种质资源,且品种间遗传多样性较好。

关键词: 蓝莓, 全基因组, SSR分子标记, SSR引物, 遗传多样性

Abstract:

Objective To address the challenges posed by morphologically ambiguous blueberry cultivars and the lack of a precise identification system, this study aimed to mine genome-wide SSR loci, analyze their characteristics, and develop novel SSR markers, thereby providing a solid foundation for accurate authentication of blueberry germplasm and assessment of genetic diversity. Method SSR loci within the 'Draper' genome were mined and analyzed using Krait software, and primers were designed with Primer 3.0. Preliminary screening of SSR marker primers was performed through bioinformatics analysis. PCR amplification was conducted using a gradually expanded blueberry germplasm collection. A combination of non-denaturing polyacrylamide gel electrophoresis (PAGE) and capillary electrophoresis was employed to screen for highly polymorphic SSR markers. Subsequently, genetic diversity analysis of blueberry germplasm was carried out using the finally selected highly polymorphic primers. Result A total of 888 906 SSR loci were identified in the 'Draper' genome. Dinucleotide repeat motifs were the dominant type, accounting for 87.80% of the total, followed by trinucleotide repeats, which represented 6.34%. Following bioinformatic primer design and preliminary screening, 103 pairs of SSR marker primers were obtained. Subsequent multi-round electrophoretic screening yielded 17 pairs of highly polymorphic SSR markers. These were used to analyze the genetic diversity of 64 blueberry germplasm accessions. A total of 204 alleles were detected. The average effective number of alleles (Ne) was 6.165, the average Shannon’s information index (I) was 1.956, and the average polymorphism information content (PIC) was 0.985, indicating that the developed SSR markers are highly polymorphic. UPGMA cluster analysis showed that the 64 blueberry accessions could be grouped into three distinct clusters at a Nei’s genetic distance of 0.000 8. Conclusion This study characterized the abundance and motif distribution of SSR loci in the blueberry genome. Seventeen highly polymorphic SSR primer pairs were developed, which proved effective for distinguishing blueberry germplasm accessions. Furthermore, the genetic diversity among blueberry cultivars was found to be high.

Key words: Vaccinium spp., whole-genome, SSR molecular marker, SSR primer, genetic diversity